Starting phenix.real_space_refine on Tue Nov 18 06:52:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6djo_7938/11_2025/6djo_7938.cif Found real_map, /net/cci-nas-00/data/ceres_data/6djo_7938/11_2025/6djo_7938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6djo_7938/11_2025/6djo_7938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6djo_7938/11_2025/6djo_7938.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6djo_7938/11_2025/6djo_7938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6djo_7938/11_2025/6djo_7938.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.99, per 1000 atoms: 0.25 Number of scatterers: 11748 At special positions: 0 Unit cell: (100.32, 76.285, 166.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 526.7 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 24 sheets defined 40.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.534A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.817A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.961A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.836A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.569A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.738A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.716A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.753A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.765A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 91 removed outlier: 3.534A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.816A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 146 removed outlier: 3.960A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.836A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.569A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.739A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.717A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.753A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 370 removed outlier: 3.766A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 370' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.534A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.816A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 146 removed outlier: 3.961A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.837A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.569A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 228 Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.738A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.717A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.753A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 370 removed outlier: 3.765A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 370' Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.535A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.816A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 3.961A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.836A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.688A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.568A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.738A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.717A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.942A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.753A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 370 removed outlier: 3.765A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 370' Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.539A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.756A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.934A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.539A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.756A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.935A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.540A pdb=" N VAL C 9 " --> pdb=" O GLY C 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.757A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.934A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.539A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.756A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.935A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 372 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3792 1.34 - 1.46: 2374 1.46 - 1.57: 5678 1.57 - 1.69: 12 1.69 - 1.81: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" C VAL D 370 " pdb=" N HIS D 371 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.46e-02 4.69e+03 1.99e+01 bond pdb=" C VAL B 370 " pdb=" N HIS B 371 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.46e-02 4.69e+03 1.32e+01 bond pdb=" C VAL C 370 " pdb=" N HIS C 371 " ideal model delta sigma weight residual 1.334 1.382 -0.047 1.46e-02 4.69e+03 1.04e+01 bond pdb=" C VAL A 370 " pdb=" N HIS A 371 " ideal model delta sigma weight residual 1.334 1.381 -0.046 1.46e-02 4.69e+03 1.00e+01 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 14972 1.52 - 3.03: 1051 3.03 - 4.55: 190 4.55 - 6.06: 50 6.06 - 7.58: 29 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 116.90 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 116.90 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 116.86 -6.36 1.70e+00 3.46e-01 1.40e+01 angle pdb=" C HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.10 103.38 6.72 1.90e+00 2.77e-01 1.25e+01 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 6829 16.77 - 33.54: 297 33.54 - 50.31: 85 50.31 - 67.08: 6 67.08 - 83.85: 3 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" C5' ADP D 802 " pdb=" O5' ADP D 802 " pdb=" PA ADP D 802 " pdb=" O2A ADP D 802 " ideal model delta sinusoidal sigma weight residual -60.00 23.86 -83.85 1 2.00e+01 2.50e-03 2.14e+01 dihedral pdb=" CA MET A 325 " pdb=" C MET A 325 " pdb=" N LYS A 326 " pdb=" CA LYS A 326 " ideal model delta harmonic sigma weight residual 180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET D 325 " pdb=" C MET D 325 " pdb=" N LYS D 326 " pdb=" CA LYS D 326 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1126 0.052 - 0.103: 579 0.103 - 0.155: 75 0.155 - 0.206: 12 0.206 - 0.258: 16 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA CYS A 257 " pdb=" N CYS A 257 " pdb=" C CYS A 257 " pdb=" CB CYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA CYS D 257 " pdb=" N CYS D 257 " pdb=" C CYS D 257 " pdb=" CB CYS D 257 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 372 " 0.260 9.50e-02 1.11e+02 1.16e-01 8.31e+00 pdb=" NE ARG D 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 372 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 372 " 0.260 9.50e-02 1.11e+02 1.16e-01 8.30e+00 pdb=" NE ARG C 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 372 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 372 " 0.259 9.50e-02 1.11e+02 1.16e-01 8.28e+00 pdb=" NE ARG B 372 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG B 372 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 372 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 372 " 0.009 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 163 2.62 - 3.19: 9991 3.19 - 3.76: 17230 3.76 - 4.33: 25357 4.33 - 4.90: 41589 Nonbonded interactions: 94330 Sorted by model distance: nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 2.053 2.170 nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 2.077 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 2.082 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 2.092 2.170 nonbonded pdb="MG MG D 801 " pdb=" O3B ADP D 802 " model vdw 2.122 2.170 ... (remaining 94325 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.900 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 12004 Z= 0.404 Angle : 0.943 7.580 16292 Z= 0.502 Chirality : 0.060 0.258 1808 Planarity : 0.008 0.116 2084 Dihedral : 10.850 83.855 4468 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.96 % Allowed : 3.18 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.17), residues: 1468 helix: -4.43 (0.10), residues: 556 sheet: -2.45 (0.41), residues: 132 loop : -2.24 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 177 TYR 0.016 0.002 TYR B 169 PHE 0.018 0.002 PHE B 31 TRP 0.029 0.004 TRP C 340 HIS 0.008 0.003 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00909 (12004) covalent geometry : angle 0.94313 (16292) hydrogen bonds : bond 0.30802 ( 372) hydrogen bonds : angle 10.27367 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 290 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8798 (ppp) cc_final: 0.8581 (ppp) REVERT: A 283 MET cc_start: 0.7802 (mmt) cc_final: 0.7519 (mmm) REVERT: B 153 LEU cc_start: 0.9050 (tp) cc_final: 0.8802 (tp) REVERT: B 296 ASN cc_start: 0.8378 (m-40) cc_final: 0.8080 (m-40) REVERT: B 367 PRO cc_start: 0.8663 (Cg_endo) cc_final: 0.8430 (Cg_exo) REVERT: C 123 MET cc_start: 0.8833 (mmm) cc_final: 0.8617 (mmt) REVERT: C 244 ASP cc_start: 0.7895 (p0) cc_final: 0.7680 (p0) REVERT: D 10 CYS cc_start: 0.8304 (t) cc_final: 0.8088 (t) REVERT: D 44 MET cc_start: 0.7523 (mmp) cc_final: 0.7091 (mmt) REVERT: D 132 MET cc_start: 0.8660 (ppp) cc_final: 0.8459 (ttp) REVERT: D 154 ASP cc_start: 0.8395 (t0) cc_final: 0.8095 (t0) REVERT: D 162 ASN cc_start: 0.8664 (m110) cc_final: 0.8431 (m110) REVERT: D 191 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8495 (tttm) REVERT: D 326 LYS cc_start: 0.8062 (pmtt) cc_final: 0.7775 (ptmt) outliers start: 12 outliers final: 9 residues processed: 301 average time/residue: 0.1285 time to fit residues: 53.3674 Evaluate side-chains 161 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 373 LYS Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 111 ASN B 162 ASN B 246 GLN C 12 ASN C 128 ASN C 137 GLN C 162 ASN D 78 ASN D 162 ASN D 246 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075837 restraints weight = 24353.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078513 restraints weight = 12577.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.080377 restraints weight = 7906.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.081661 restraints weight = 5578.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082544 restraints weight = 4297.178| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12004 Z= 0.151 Angle : 0.666 6.626 16292 Z= 0.332 Chirality : 0.048 0.184 1808 Planarity : 0.005 0.037 2084 Dihedral : 8.265 78.184 1702 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.99 % Allowed : 8.28 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.18), residues: 1468 helix: -3.30 (0.14), residues: 584 sheet: -2.85 (0.35), residues: 164 loop : -1.55 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 312 TYR 0.009 0.001 TYR A 169 PHE 0.012 0.001 PHE B 375 TRP 0.016 0.002 TRP C 340 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00343 (12004) covalent geometry : angle 0.66621 (16292) hydrogen bonds : bond 0.04357 ( 372) hydrogen bonds : angle 6.44068 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7487 (mmm) cc_final: 0.5869 (mpp) REVERT: B 41 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7697 (mp10) REVERT: B 82 MET cc_start: 0.8600 (tpt) cc_final: 0.8374 (tpt) REVERT: B 367 PRO cc_start: 0.8608 (Cg_endo) cc_final: 0.8379 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6239 (mmtt) REVERT: C 123 MET cc_start: 0.8708 (mmm) cc_final: 0.8231 (mmm) REVERT: C 202 THR cc_start: 0.8914 (p) cc_final: 0.8569 (t) REVERT: C 205 GLU cc_start: 0.7254 (mp0) cc_final: 0.7038 (mt-10) REVERT: C 314 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8138 (tm-30) REVERT: D 10 CYS cc_start: 0.8285 (t) cc_final: 0.8030 (t) REVERT: D 132 MET cc_start: 0.8319 (ppp) cc_final: 0.8023 (ttp) REVERT: D 142 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8680 (mt) REVERT: D 154 ASP cc_start: 0.8405 (t0) cc_final: 0.7910 (t0) REVERT: D 191 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8540 (tttm) REVERT: D 205 GLU cc_start: 0.7537 (mp0) cc_final: 0.7324 (mp0) outliers start: 25 outliers final: 9 residues processed: 200 average time/residue: 0.1009 time to fit residues: 30.0651 Evaluate side-chains 140 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 111 ASN C 12 ASN C 246 GLN D 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.074849 restraints weight = 24284.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077534 restraints weight = 12596.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079408 restraints weight = 7918.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080700 restraints weight = 5584.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081555 restraints weight = 4303.379| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12004 Z= 0.173 Angle : 0.629 6.423 16292 Z= 0.309 Chirality : 0.048 0.190 1808 Planarity : 0.004 0.031 2084 Dihedral : 7.484 75.519 1682 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.99 % Allowed : 10.19 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.20), residues: 1468 helix: -2.51 (0.18), residues: 572 sheet: -2.55 (0.36), residues: 180 loop : -1.13 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.010 0.001 TYR D 143 PHE 0.011 0.001 PHE B 375 TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00396 (12004) covalent geometry : angle 0.62939 (16292) hydrogen bonds : bond 0.03917 ( 372) hydrogen bonds : angle 5.84882 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7505 (mmm) cc_final: 0.5866 (mpp) REVERT: A 137 GLN cc_start: 0.8426 (mt0) cc_final: 0.8078 (mt0) REVERT: A 176 MET cc_start: 0.8300 (mmm) cc_final: 0.8080 (mmt) REVERT: A 325 MET cc_start: 0.8172 (ppp) cc_final: 0.7086 (ppp) REVERT: B 41 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7787 (mp10) REVERT: B 44 MET cc_start: 0.6347 (mmm) cc_final: 0.4332 (mpp) REVERT: B 367 PRO cc_start: 0.8720 (Cg_endo) cc_final: 0.8476 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6939 (mmtt) cc_final: 0.6321 (mmtt) REVERT: C 132 MET cc_start: 0.8297 (ppp) cc_final: 0.7949 (ppp) REVERT: C 202 THR cc_start: 0.8978 (p) cc_final: 0.8619 (t) REVERT: D 132 MET cc_start: 0.8416 (ppp) cc_final: 0.8035 (ttp) REVERT: D 142 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8677 (mt) REVERT: D 154 ASP cc_start: 0.8367 (t0) cc_final: 0.7980 (t0) REVERT: D 201 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8222 (p) REVERT: D 205 GLU cc_start: 0.7519 (mp0) cc_final: 0.7161 (mp0) outliers start: 25 outliers final: 10 residues processed: 150 average time/residue: 0.0924 time to fit residues: 21.3336 Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 87 optimal weight: 0.0770 chunk 123 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075201 restraints weight = 24233.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077932 restraints weight = 12559.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.079814 restraints weight = 7834.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081076 restraints weight = 5519.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082000 restraints weight = 4269.000| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12004 Z= 0.149 Angle : 0.594 6.318 16292 Z= 0.289 Chirality : 0.047 0.165 1808 Planarity : 0.004 0.030 2084 Dihedral : 7.027 73.322 1676 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.59 % Allowed : 11.46 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.21), residues: 1468 helix: -2.09 (0.20), residues: 572 sheet: -2.33 (0.32), residues: 228 loop : -0.77 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.007 0.001 TYR D 306 PHE 0.014 0.001 PHE B 223 TRP 0.013 0.002 TRP C 340 HIS 0.008 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00344 (12004) covalent geometry : angle 0.59393 (16292) hydrogen bonds : bond 0.03398 ( 372) hydrogen bonds : angle 5.51103 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7648 (mmm) cc_final: 0.5838 (mpp) REVERT: A 121 GLN cc_start: 0.8689 (tm-30) cc_final: 0.8367 (tm-30) REVERT: A 137 GLN cc_start: 0.8351 (mt0) cc_final: 0.8006 (mt0) REVERT: A 176 MET cc_start: 0.8240 (mmm) cc_final: 0.8006 (mmt) REVERT: A 325 MET cc_start: 0.8117 (ppp) cc_final: 0.7339 (ppp) REVERT: B 41 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7948 (mp10) REVERT: B 44 MET cc_start: 0.6324 (mmm) cc_final: 0.4314 (mpp) REVERT: B 367 PRO cc_start: 0.8699 (Cg_endo) cc_final: 0.8474 (Cg_exo) REVERT: C 113 LYS cc_start: 0.6925 (mmtt) cc_final: 0.6329 (mmtt) REVERT: C 132 MET cc_start: 0.8199 (ppp) cc_final: 0.7875 (ppp) REVERT: C 202 THR cc_start: 0.8645 (p) cc_final: 0.8327 (t) REVERT: D 132 MET cc_start: 0.8366 (ppp) cc_final: 0.7976 (ttp) REVERT: D 142 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8630 (mt) REVERT: D 154 ASP cc_start: 0.8315 (t0) cc_final: 0.7977 (t0) REVERT: D 201 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8237 (p) outliers start: 20 outliers final: 10 residues processed: 143 average time/residue: 0.0833 time to fit residues: 19.0851 Evaluate side-chains 127 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 0.0470 chunk 142 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.087886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074471 restraints weight = 24247.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077270 restraints weight = 12547.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.079186 restraints weight = 7853.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.080345 restraints weight = 5563.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.081285 restraints weight = 4378.573| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12004 Z= 0.167 Angle : 0.600 6.277 16292 Z= 0.292 Chirality : 0.047 0.162 1808 Planarity : 0.004 0.030 2084 Dihedral : 6.882 73.117 1674 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.83 % Allowed : 11.46 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.22), residues: 1468 helix: -1.91 (0.20), residues: 572 sheet: -2.17 (0.37), residues: 172 loop : -0.53 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.007 0.001 TYR A 166 PHE 0.031 0.001 PHE C 223 TRP 0.013 0.002 TRP C 340 HIS 0.009 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00385 (12004) covalent geometry : angle 0.59963 (16292) hydrogen bonds : bond 0.03389 ( 372) hydrogen bonds : angle 5.38855 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7627 (mmm) cc_final: 0.5830 (mpp) REVERT: A 121 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 137 GLN cc_start: 0.8288 (mt0) cc_final: 0.7929 (mt0) REVERT: A 325 MET cc_start: 0.7974 (ppp) cc_final: 0.7314 (ppp) REVERT: B 41 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: B 44 MET cc_start: 0.6269 (mmm) cc_final: 0.4267 (mpp) REVERT: B 292 ASP cc_start: 0.8124 (t0) cc_final: 0.7781 (t0) REVERT: C 113 LYS cc_start: 0.6909 (mmtt) cc_final: 0.6292 (mmtt) REVERT: C 132 MET cc_start: 0.8203 (ppp) cc_final: 0.7849 (ppp) REVERT: C 202 THR cc_start: 0.8689 (p) cc_final: 0.8362 (t) REVERT: D 132 MET cc_start: 0.8415 (ppp) cc_final: 0.7970 (ttp) REVERT: D 142 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8681 (mt) REVERT: D 154 ASP cc_start: 0.8337 (t0) cc_final: 0.7944 (t0) REVERT: D 201 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8224 (p) REVERT: D 205 GLU cc_start: 0.7437 (mp0) cc_final: 0.7172 (mp0) outliers start: 23 outliers final: 15 residues processed: 137 average time/residue: 0.0863 time to fit residues: 18.9721 Evaluate side-chains 132 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 0.0980 chunk 60 optimal weight: 4.9990 chunk 142 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.088167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.074909 restraints weight = 24320.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077694 restraints weight = 12526.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.079624 restraints weight = 7830.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080918 restraints weight = 5506.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.081767 restraints weight = 4232.667| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12004 Z= 0.143 Angle : 0.579 6.220 16292 Z= 0.280 Chirality : 0.047 0.157 1808 Planarity : 0.003 0.035 2084 Dihedral : 6.713 72.118 1674 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.51 % Allowed : 12.10 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.22), residues: 1468 helix: -1.67 (0.21), residues: 568 sheet: -2.06 (0.37), residues: 172 loop : -0.42 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 312 TYR 0.006 0.001 TYR A 166 PHE 0.015 0.001 PHE C 223 TRP 0.012 0.001 TRP C 340 HIS 0.006 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00333 (12004) covalent geometry : angle 0.57925 (16292) hydrogen bonds : bond 0.03248 ( 372) hydrogen bonds : angle 5.26945 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.7612 (mmm) cc_final: 0.5829 (mpp) REVERT: A 325 MET cc_start: 0.7883 (ppp) cc_final: 0.7275 (ppp) REVERT: B 44 MET cc_start: 0.6222 (mmm) cc_final: 0.4234 (mpp) REVERT: B 292 ASP cc_start: 0.8098 (t0) cc_final: 0.7752 (t0) REVERT: C 113 LYS cc_start: 0.6916 (mmtt) cc_final: 0.6335 (mmtt) REVERT: C 132 MET cc_start: 0.8179 (ppp) cc_final: 0.7827 (ppp) REVERT: C 325 MET cc_start: 0.8229 (ppp) cc_final: 0.7654 (ppp) REVERT: D 132 MET cc_start: 0.8421 (ppp) cc_final: 0.8006 (ttp) REVERT: D 142 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8670 (mt) REVERT: D 154 ASP cc_start: 0.8331 (t0) cc_final: 0.7963 (t0) REVERT: D 162 ASN cc_start: 0.8420 (m-40) cc_final: 0.8043 (m-40) REVERT: D 201 VAL cc_start: 0.8520 (OUTLIER) cc_final: 0.8194 (p) REVERT: D 205 GLU cc_start: 0.7438 (mp0) cc_final: 0.7123 (mp0) outliers start: 19 outliers final: 15 residues processed: 132 average time/residue: 0.0826 time to fit residues: 17.8179 Evaluate side-chains 132 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.075513 restraints weight = 24200.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.078303 restraints weight = 12462.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.080230 restraints weight = 7803.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081524 restraints weight = 5510.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082423 restraints weight = 4251.173| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12004 Z= 0.130 Angle : 0.568 6.158 16292 Z= 0.275 Chirality : 0.046 0.156 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.508 70.685 1674 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.75 % Allowed : 12.42 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.22), residues: 1468 helix: -1.53 (0.21), residues: 572 sheet: -1.94 (0.37), residues: 172 loop : -0.30 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 206 TYR 0.007 0.001 TYR A 166 PHE 0.011 0.001 PHE C 223 TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00304 (12004) covalent geometry : angle 0.56833 (16292) hydrogen bonds : bond 0.03126 ( 372) hydrogen bonds : angle 5.12367 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.481 Fit side-chains REVERT: A 44 MET cc_start: 0.7564 (mmm) cc_final: 0.5720 (mpp) REVERT: A 325 MET cc_start: 0.7748 (ppp) cc_final: 0.7125 (ppp) REVERT: B 44 MET cc_start: 0.6108 (mmm) cc_final: 0.4129 (mpp) REVERT: B 292 ASP cc_start: 0.8042 (t0) cc_final: 0.7725 (t0) REVERT: B 313 MET cc_start: 0.7886 (tpp) cc_final: 0.7667 (tpp) REVERT: C 113 LYS cc_start: 0.6885 (mmtt) cc_final: 0.6309 (mmtt) REVERT: C 132 MET cc_start: 0.8159 (ppp) cc_final: 0.7806 (ppp) REVERT: C 270 GLU cc_start: 0.7861 (tp30) cc_final: 0.7657 (tm-30) REVERT: C 325 MET cc_start: 0.8181 (ppp) cc_final: 0.7647 (ppp) REVERT: D 132 MET cc_start: 0.8397 (ppp) cc_final: 0.7952 (ttp) REVERT: D 142 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8658 (mt) REVERT: D 154 ASP cc_start: 0.8327 (t0) cc_final: 0.7970 (t0) REVERT: D 162 ASN cc_start: 0.8416 (m-40) cc_final: 0.8075 (m-40) REVERT: D 201 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8082 (p) REVERT: D 205 GLU cc_start: 0.7347 (mp0) cc_final: 0.7025 (mp0) REVERT: D 327 ILE cc_start: 0.8923 (mt) cc_final: 0.8689 (tt) outliers start: 22 outliers final: 16 residues processed: 140 average time/residue: 0.0874 time to fit residues: 19.6050 Evaluate side-chains 131 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076406 restraints weight = 24128.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.079216 restraints weight = 12394.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.081159 restraints weight = 7727.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.082479 restraints weight = 5442.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.083397 restraints weight = 4181.247| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12004 Z= 0.105 Angle : 0.556 6.795 16292 Z= 0.267 Chirality : 0.045 0.155 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.228 60.862 1674 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.35 % Allowed : 13.30 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1468 helix: -1.35 (0.21), residues: 572 sheet: -1.82 (0.37), residues: 172 loop : -0.22 (0.25), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.006 0.001 TYR A 306 PHE 0.013 0.001 PHE B 223 TRP 0.011 0.001 TRP C 340 HIS 0.005 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00242 (12004) covalent geometry : angle 0.55632 (16292) hydrogen bonds : bond 0.03007 ( 372) hydrogen bonds : angle 4.98187 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.439 Fit side-chains REVERT: A 44 MET cc_start: 0.7517 (mmm) cc_final: 0.5444 (mtm) REVERT: A 325 MET cc_start: 0.7698 (ppp) cc_final: 0.7021 (ppp) REVERT: B 44 MET cc_start: 0.6072 (mmm) cc_final: 0.4137 (mpp) REVERT: B 82 MET cc_start: 0.8870 (tpp) cc_final: 0.8470 (mmm) REVERT: B 292 ASP cc_start: 0.8048 (t0) cc_final: 0.7835 (t0) REVERT: B 313 MET cc_start: 0.7878 (tpp) cc_final: 0.7650 (tpp) REVERT: C 113 LYS cc_start: 0.6891 (mmtt) cc_final: 0.6358 (mmtt) REVERT: C 132 MET cc_start: 0.8135 (ppp) cc_final: 0.7791 (ppp) REVERT: C 325 MET cc_start: 0.8118 (ppp) cc_final: 0.7589 (ppp) REVERT: D 132 MET cc_start: 0.8331 (ppp) cc_final: 0.7633 (ttp) REVERT: D 142 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8607 (mt) REVERT: D 154 ASP cc_start: 0.8254 (t0) cc_final: 0.8026 (t70) REVERT: D 162 ASN cc_start: 0.8401 (m-40) cc_final: 0.8154 (m110) REVERT: D 205 GLU cc_start: 0.7343 (mp0) cc_final: 0.6993 (mp0) outliers start: 17 outliers final: 12 residues processed: 137 average time/residue: 0.0791 time to fit residues: 17.6155 Evaluate side-chains 129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.074028 restraints weight = 24210.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.076753 restraints weight = 12668.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.078633 restraints weight = 7962.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079907 restraints weight = 5637.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080813 restraints weight = 4351.394| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12004 Z= 0.200 Angle : 0.614 6.892 16292 Z= 0.301 Chirality : 0.048 0.150 1808 Planarity : 0.004 0.028 2084 Dihedral : 6.434 65.697 1674 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.91 % Allowed : 13.22 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.22), residues: 1468 helix: -1.33 (0.21), residues: 568 sheet: -1.78 (0.38), residues: 172 loop : -0.26 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.009 0.001 TYR B 279 PHE 0.011 0.001 PHE B 223 TRP 0.011 0.002 TRP C 340 HIS 0.014 0.002 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00463 (12004) covalent geometry : angle 0.61390 (16292) hydrogen bonds : bond 0.03401 ( 372) hydrogen bonds : angle 5.12850 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.453 Fit side-chains REVERT: A 44 MET cc_start: 0.7528 (mmm) cc_final: 0.5705 (mpp) REVERT: A 325 MET cc_start: 0.7798 (ppp) cc_final: 0.7572 (ptp) REVERT: B 44 MET cc_start: 0.6296 (mmm) cc_final: 0.4371 (mpp) REVERT: B 292 ASP cc_start: 0.8095 (t0) cc_final: 0.7794 (t0) REVERT: C 113 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6258 (mmtt) REVERT: C 132 MET cc_start: 0.8163 (ppp) cc_final: 0.7589 (ppp) REVERT: C 291 LYS cc_start: 0.6892 (mptt) cc_final: 0.6495 (mptt) REVERT: C 325 MET cc_start: 0.8137 (ppp) cc_final: 0.7653 (ppp) REVERT: D 132 MET cc_start: 0.8532 (ppp) cc_final: 0.8066 (ttp) REVERT: D 142 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8600 (mm) REVERT: D 154 ASP cc_start: 0.8317 (t0) cc_final: 0.7938 (t0) REVERT: D 162 ASN cc_start: 0.8468 (m-40) cc_final: 0.8197 (m110) REVERT: D 205 GLU cc_start: 0.7358 (mp0) cc_final: 0.7025 (mp0) outliers start: 24 outliers final: 20 residues processed: 141 average time/residue: 0.0848 time to fit residues: 19.2261 Evaluate side-chains 144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 0.0010 chunk 51 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075699 restraints weight = 24203.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078503 restraints weight = 12447.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.080436 restraints weight = 7734.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.081738 restraints weight = 5428.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082658 restraints weight = 4162.449| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12004 Z= 0.119 Angle : 0.578 7.512 16292 Z= 0.281 Chirality : 0.046 0.152 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.243 62.635 1674 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.27 % Allowed : 14.25 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.23), residues: 1468 helix: -1.20 (0.22), residues: 572 sheet: -1.69 (0.33), residues: 228 loop : -0.18 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 312 TYR 0.013 0.001 TYR B 279 PHE 0.011 0.001 PHE B 223 TRP 0.012 0.001 TRP C 340 HIS 0.015 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00276 (12004) covalent geometry : angle 0.57784 (16292) hydrogen bonds : bond 0.03139 ( 372) hydrogen bonds : angle 5.03962 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.429 Fit side-chains REVERT: A 44 MET cc_start: 0.7492 (mmm) cc_final: 0.5431 (mtm) REVERT: A 325 MET cc_start: 0.7736 (ppp) cc_final: 0.7073 (ppp) REVERT: B 44 MET cc_start: 0.6104 (mmm) cc_final: 0.4129 (mpp) REVERT: B 292 ASP cc_start: 0.8052 (t0) cc_final: 0.7851 (t0) REVERT: C 113 LYS cc_start: 0.6908 (mmtt) cc_final: 0.6321 (mmtt) REVERT: C 132 MET cc_start: 0.8166 (ppp) cc_final: 0.7832 (ppp) REVERT: C 205 GLU cc_start: 0.7402 (mp0) cc_final: 0.7169 (mp0) REVERT: C 291 LYS cc_start: 0.6895 (mptt) cc_final: 0.6500 (mptt) REVERT: C 325 MET cc_start: 0.8070 (ppp) cc_final: 0.7600 (ppp) REVERT: D 132 MET cc_start: 0.8410 (ppp) cc_final: 0.7937 (ttp) REVERT: D 142 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8673 (mt) REVERT: D 154 ASP cc_start: 0.8205 (t0) cc_final: 0.7957 (t70) REVERT: D 162 ASN cc_start: 0.8416 (m-40) cc_final: 0.8085 (m-40) REVERT: D 205 GLU cc_start: 0.7382 (mp0) cc_final: 0.7030 (mp0) outliers start: 16 outliers final: 15 residues processed: 130 average time/residue: 0.0831 time to fit residues: 17.5136 Evaluate side-chains 136 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 97 optimal weight: 0.0170 chunk 98 optimal weight: 1.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.076293 restraints weight = 24107.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.079086 restraints weight = 12557.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.081024 restraints weight = 7848.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082338 restraints weight = 5527.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.083260 restraints weight = 4242.837| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12004 Z= 0.111 Angle : 0.572 8.642 16292 Z= 0.276 Chirality : 0.045 0.149 1808 Planarity : 0.003 0.027 2084 Dihedral : 6.034 58.611 1674 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.59 % Allowed : 14.09 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.23), residues: 1468 helix: -1.03 (0.22), residues: 572 sheet: -1.63 (0.32), residues: 228 loop : -0.12 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 312 TYR 0.011 0.001 TYR B 279 PHE 0.010 0.001 PHE B 223 TRP 0.011 0.001 TRP C 340 HIS 0.014 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00257 (12004) covalent geometry : angle 0.57214 (16292) hydrogen bonds : bond 0.03020 ( 372) hydrogen bonds : angle 4.95840 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1707.75 seconds wall clock time: 30 minutes 31.38 seconds (1831.38 seconds total)